24 August, 2019

Background

Required

Version control

Version control

Version control

  • large space requirements
  • difficult to collaborate

Git

Git - overview

  • Git - is a distributed version control system

  • Git - stores snapshots of the filesystem

    • commits

  • The system consists of three trees:

Git - overview

Files can be in one of four states:

  • untracked

Git - overview

Files can be in one of four states:

  • untracked
  • staged

Git - overview

Files can be in one of four states:

  • untracked
  • staged
  • committed

Git - overview

Files can be in one of four states:

  • untracked
  • staged
  • committed
  • modified

Git - overview

Git - overview

Git - configuration

This is a once off action

git config --global user.name "Your name"
git config --global user.email "your_email@whatever.com"

Git - new repository

mkdir ~/tmp/Test_repo
cd ~/tmp/Test_repo
git init
## Initialized empty Git repository in /home/murray/tmp/Test_repo/.git/

RStudio

Git - adding content

Create a file (text, code etc)

  • those using R, call it analysis.R
x=seq(1, 10, len=1)
y=40*2 + rnorm(10,0,5)
plot(x,y)

Otherwise, create any kind of file (in the folder we just created)

Git - adding content

Stage the changes (add)

git add <file(s)>

For example:

git add analysis.R

RStudio

Git - adding content

Git - .gitignore

RStudio

Git - committing

git commit -m 'Initial commit'
## [master (root-commit) 5f2f4eb] Initial commit
##  1 file changed, 3 insertions(+)
##  create mode 100644 analysis.R

RStudio

Git - committing

Git - additional edits

  • Make some changes to the file, stage (add) and commit
x=seq(1, 10, len=1)
y=40*2 + rnorm(10,0,5)
plot(x,y)
summary(x)
## [master 93a12d7] Added summary for x
##  1 file changed, 1 insertion(+)

Git - additional edits

  • Let remove the summary(x) and add it to another file, stage (add) and commit

analysis.R

x=seq(1, 10, len=1)
y=40*2 + rnorm(10,0,5)
plot(x,y)

summary.R

summary(x)
summary(y)
## [master b729ed7] Added summaries for x and y
##  2 files changed, 2 insertions(+), 1 deletion(-)
##  create mode 100644 summary.R

Git - additional edits

Git - history (logs)

git log --oneline --graph --decorate
## * b729ed7 (HEAD -> master) Added summaries for x and y
## * 93a12d7 Added summary for x
## * 5f2f4eb Initial commit

RStudio

Git - tags

git tag -a <tag> -m <message>

For example:

git tag -a 'V.1' -m 'Version 1'

RStudio

Git - tags

Rolling back to previous snapshots

Git - rolling back

  1. checkout

  2. reset

  3. revert

Git - checkout

git checkout #

# is a commit or tag name

git checkout  93a1

RStudio

Git - checkout

Git - checkout

Restore the HEAD to the tip of master

git checkout master
## Previous HEAD position was 93a12d7 Added summary for x
## Switched to branch 'master'

Git - checkout

Git - reset

git reset --hard #

# is a commit or tag name

cd ~/tmp/Test_repo
git reset --hard  93a1

RStudio

Git - reset

Git - reset

Restore HEAD to the tag V.1

git reset --hard V.1
## HEAD is now at b729ed7 Added summaries for x and y

Git - reset

Git - revert

git revert HEAD --no-edit
## [master 011113f] Revert "Added summaries for x and y"
##  Date: Sat Aug 24 17:32:39 2019 +1000
##  2 files changed, 1 insertion(+), 2 deletions(-)
##  delete mode 100644 summary.R

RStudio

Git - revert

Git - revert multiples

command line

git revert --no-commit HEAD
git revert --no-commit HEAD~1
git commit -m 'Rolled back'

RStudio

Branching

Git - new branch

git checkout -b <Name>

For example

git checkout -b Experimental

RStudio

Git - new branch

Git - branch

We are on the new branch

  • add or edit some content
    • stage and commit
x=seq(1, 10, len=1)
y=40*2 + rnorm(10,0,5)
plot(x,y)
summary(x)
mean(x)

Otherwise, create any kind of file (in the folder we just created)

Git - branch

Git - switch branch

git checkout <Name>

For example:

git checkout master

RStudio

Git - switch branch

Git - branch

We are on the master branch

  • add another file (test.R)
    • stage and commit
mean(c(1,2,3))

Otherwise, create any kind of file

Git - branch

Git - branch log

git log --online --graph --decorate --all

RStudio

Git - diff

git diff master <branch>

For example:

git diff master Experimental
## diff --git a/analysis.R b/analysis.R
## index 9b5dda9..660b1bc 100644
## --- a/analysis.R
## +++ b/analysis.R
## @@ -2,3 +2,4 @@ x=seq(1, 10, len=1)
##  y=40*2 + rnorm(10,0,5)
##  plot(x,y)
##  summary(x)
## +mean(x)
## diff --git a/test.R b/test.R
## deleted file mode 100644
## index 0242716..0000000
## --- a/test.R
## +++ /dev/null
## @@ -1 +0,0 @@
## -mean(c(1,2,3))

Git - merge branches

git merge <Name>

For example:

cd ~/tmp/Test_repo
git merge Experimental -m 'Merge master and Experimental'
## Merge made by the 'recursive' strategy.
##  analysis.R | 1 +
##  1 file changed, 1 insertion(+)

RStudio

Use the shell

Git - merge branches

Remote repositories and github

New remote repo

New remote repo

Set remote

cd ~/tmp/Test_repo
git remote add origin https://github.com/pcinereus/Test.git
git push -u origin master

RStudio

Use the shell ….. Um Luke!

Set remote

Github - collaborate

Git - another commit

Lets make a small change to one of the files..

mean(c(1,2,3))
sd(c(1,2,3))



Otherwise, create any kind of file

Git - another commit

Git - push to repo

git push -u origin master

Clone a repo

git clone <git name> <local name>

RStudio

Git - pull

Before making any changes that you intend to push, it is advisable that you pull to get the latest from the remote

git pull -v origin master

Playtime

  • Clone the Test repo of the person next to you

  • Make a change, commit, push

  • Pull the changes of your neighbour

  • Try making a branch

Resources

Useful resources